Updating to VCF 4.0

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3770 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java

@@ -177,13 +177,13 @@ public class VariantContextAdaptors {
 
                 Map<String, String> fields = new HashMap<String, String>();
                 for ( Map.Entry<String, String> e : vcfG.getFields().entrySet() ) {
-                    // todo -- fixme if we put GQ and GF into key itself
+                    // todo -- fixme if we put GQ and FT into key itself
                     if ( ! e.getKey().equals(VCFConstants.GENOTYPE_QUALITY_KEY) && ! e.getKey().equals(VCFConstants.GENOTYPE_FILTER_KEY) )
                         fields.put(e.getKey(), e.getValue());
                 }
 
                 Set<String> genotypeFilters = new HashSet<String>();
-                if ( vcfG.isFiltered() ) // setup the FL genotype filter fields
+                if ( vcfG.isFiltered() ) // setup the genotype filter fields
                     genotypeFilters.addAll(Arrays.asList(vcfG.getFields().get(VCFConstants.GENOTYPE_FILTER_KEY).split(";")));
 
                 double qual = vcfG.isMissingQual() ? VariantContext.NO_NEG_LOG_10PERROR : vcfG.getNegLog10PError();

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -142,7 +142,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
         hInfo.add(new VCFHeaderLine("annotatorReference", getToolkit().getArguments().referenceFile.getName()));
         hInfo.addAll(engine.getVCFAnnotationDescriptions());
 
-        vcfWriter = new VCFWriter(out);
+        vcfWriter = new VCFWriter(out, true);
         VCFHeader vcfHeader = new VCFHeader(hInfo, samples);
         vcfWriter.writeHeader(vcfHeader);
 

java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java

@@ -15,7 +15,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("92369e62b3bade625992bc1741e9367a"));
+                Arrays.asList("179af890ec44e5460188839b3bd6c563"));
         executeTest("test file has annotations, not asking for annotations, #1", spec);
     }
 
@@ -23,7 +23,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("1a394cdace4ff7698b603c2252ee9365"));
+                Arrays.asList("b61609288c0b5b2ea3c1b367f00884e0"));
         executeTest("test file has annotations, not asking for annotations, #2", spec);
     }
 
@@ -31,7 +31,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("5a8c9c18da89b052e7f3797cd391bff6"));
+                Arrays.asList("e9b2ba7aa5fda65424956eadbd1cd4de"));
         executeTest("test file has annotations, asking for annotations, #1", spec);
     }
 
@@ -39,7 +39,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testHasAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("0c8607c69d761bd058b944d1e98708b6"));
+                Arrays.asList("07c7997177e8a41a9fad91b4d2dc3e12"));
         executeTest("test file has annotations, asking for annotations, #2", spec);
     }
 
@@ -47,7 +47,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsNotAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("006642aabd41e806d3ea64bf5441f1d2"));
+                Arrays.asList("a56aaddedf6698c57a5a7b56bd476d97"));
         executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
     }
 
@@ -55,7 +55,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsNotAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("c66ed83d2a981c43546d05120809ed57"));
+                Arrays.asList("ad77d9aa195d9f13fdf0bb33b39772e1"));
         executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
     }
 
@@ -63,7 +63,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking1() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
-                Arrays.asList("3b570e13bd0e1cb5750da268178ce656"));
+                Arrays.asList("b7e863281e781b3c947c7c77c9a8c322"));
         executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
     }
 
@@ -71,7 +71,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoAnnotsAsking2() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
-                Arrays.asList("42e9c57cd5d266fd7837354fc8495176"));
+                Arrays.asList("13280e9bbc46d1b261d84f2286ac0627"));
         executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
     }
 
@@ -79,7 +79,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testNoReads() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
-                Arrays.asList("374da32e1b9540bfe8ee6ea5b896babd"));
+                Arrays.asList("027fc7227d900583546161a12e222c83"));
         executeTest("not passing it any reads", spec);
     }
 
@@ -87,7 +87,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
     public void testDBTag() {
         WalkerTestSpec spec = new WalkerTestSpec(
                 baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
-                Arrays.asList("39a6b268e3edc1eee5f71d77460e448e"));
+                Arrays.asList("1dc170cf522193a791026f0db77fe938"));
         executeTest("getting DB tag", spec);
     }
 }